Date: Mon, 21 Aug 2023 14:35:01 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 0e8f22496e31 - main - biology/star: Fix SIMD issue on non-amd64 Message-ID: <202308211435.37LEZ1SA030804@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=0e8f22496e314bf6c0f863722217eb8bebef9cf2 commit 0e8f22496e314bf6c0f863722217eb8bebef9cf2 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2023-08-21 14:33:20 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2023-08-21 14:33:20 +0000 biology/star: Fix SIMD issue on non-amd64 Also remove some extraneous build flags from upstream Makefile PR: 273240 Reported by: dizzy --- biology/star/Makefile | 9 ++------- biology/star/files/patch-Makefile | 12 +++++++----- 2 files changed, 9 insertions(+), 12 deletions(-) diff --git a/biology/star/Makefile b/biology/star/Makefile index 6172318b1e7d..968caa762551 100644 --- a/biology/star/Makefile +++ b/biology/star/Makefile @@ -1,5 +1,6 @@ PORTNAME= STAR DISTVERSION= 2.7.11a +PORTREVISION= 1 CATEGORIES= biology PKGNAMEPREFIX= rna- @@ -26,7 +27,7 @@ USE_GITHUB= yes GH_ACCOUNT= alexdobin WRKSRC_SUBDIR= source -MAKE_FLAGS= HTSLIB='' +MAKE_FLAGS= HTSLIB='' CXXFLAGS_SIMD="" PLIST_FILES= bin/STAR @@ -44,12 +45,6 @@ post-patch: ${WRKSRC}/bam_cat.h \ ${WRKSRC}/signalFromBAM.h -.include <bsd.port.options.mk> - -.if ${ARCH} != amd64 -MAKE_FLAGS+= CXXFLAGS_SIMD="" -.endif - do-install: ${INSTALL_PROGRAM} ${WRKSRC}/STAR ${STAGEDIR}${PREFIX}/bin diff --git a/biology/star/files/patch-Makefile b/biology/star/files/patch-Makefile index c9943e2e73bc..55d592e70c2f 100644 --- a/biology/star/files/patch-Makefile +++ b/biology/star/files/patch-Makefile @@ -1,6 +1,6 @@ ---- Makefile.orig 2022-11-01 14:50:35 UTC +--- Makefile.orig 2023-08-15 19:21:58 UTC +++ Makefile -@@ -11,6 +11,10 @@ CXXFLAGSextra ?= +@@ -11,14 +11,19 @@ CXXFLAGSextra ?= # user may define the compiler CXX ?= g++ @@ -9,9 +9,11 @@ +HTSLIB ?= htslib + # pre-defined flags - LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz - LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz -@@ -18,7 +22,8 @@ LDFLAGS_Mac :=-pthread -lz htslib/libhts.a +-LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz +-LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz ++LDFLAGS_shared := -pthread -lhts -lz ++LDFLAGS_static := -static -pthread -lhts -lz + LDFLAGS_Mac :=-pthread -lz htslib/libhts.a LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a LDFLAGS_gdb := $(LDFLAGS_shared)
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